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[hg] galaxy 3356: First pass at allowing explicit datatype conve...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c64ef44ed4c5 changeset: 3356:c64ef44ed4c5 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Feb 08 12:45:28 2010 -0500 description: First pass at allowing explicit datatype conversion to be specified. This can be used for e.g. providing a tool with a non-metadata based index file. Defined as part of a DataToolParameter: <param name="input1" type="interval" label="An Interval File"> <converter name='input1_as_a_bed_file' type='bed'/> </param> Both the original input as well as the converted dataset can be accessed like: <command>some_binary $input1 $input1_as_a_bed_file </command> if $input1 is already BED, it will be used for input1_as_a_bed_file. The name is be placed in the dictionary space of the data input parameter's parent; so for Grouping objects, e.g. a repeat: <repeat name="queries" title="Query"> <param name="input2" type="data" label="Select" > <converter name='input2_as_a_bed_file' type='bed'/> </param> </repeat> is accessed like (putting both the original and converted dataset as arguments on the command line): <command> ... #for $q in $queries ${q.input2} ${q.input2_as_a_bed_file} #end for ... </command> See notes in code in commit for additional comments. diffstat: lib/galaxy/tools/__init__.py | 28 ++++++++++++++++++++++++ lib/galaxy/tools/actions/__init__.py | 41 +++++++++++++++++++++++++++++------ lib/galaxy/tools/parameters/basic.py | 13 +++++++++- 3 files changed, 73 insertions(+), 9 deletions(-) diffs (147 lines): diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Mon Feb 08 12:45:28 2010 -0500 @@ -1198,6 +1198,28 @@ current = values["__current_case__"] wrap_values( input.cases[current].inputs, values ) elif isinstance( input, DataToolParameter ): + ##FIXME: We're populating param_dict with converters when wrapping values, + ##this should happen as a separate step before wrapping (or call this wrapping step something more generic) + ##(but iterating this same list twice would be wasteful) + #add explicit converters by name to current parent + for converter_name, converter_extensions, converter_datatypes in input.converters: + #if we are at building cmdline step, then converters have already executed + conv_ext, converted_dataset = input_values[ input.name ].find_conversion_destination( converter_datatypes ) + #when dealing with optional inputs, we'll provide a valid extension to be used for None converted dataset + if not conv_ext: + conv_ext = converter_extensions[0] + #input_values[ input.name ] is None when optional dataset, + #'conversion' of optional dataset should create wrapper around NoneDataset for converter output + if input_values[ input.name ] and not converted_dataset: + #input that converter is based from has a value, but converted dataset does not exist + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_values[ input.name ].extension, converter_extensions ) + else: + input_values[ converter_name ] = \ + DatasetFilenameWrapper( converted_dataset, + datatypes_registry = self.app.datatypes_registry, + tool = Bunch( converter_name = Bunch( extensions = conv_ext ) ), #trick wrapper into using target conv ext (when None) without actually being a tool parameter + name = converter_name ) + #wrap actual input dataset input_values[ input.name ] = \ DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, @@ -1212,6 +1234,12 @@ # tools (e.g. UCSC) should really be handled in a special way. if self.check_values: wrap_values( self.inputs, param_dict ) + ###FIXME: when self.check_values==True, input datasets are being wrapped twice + ### (above and below, creating 2 separate DatasetFilenameWrapper objects - first is overwritten by second), + ###is this necessary? - if we get rid of this way to access children, can we stop this redundancy, or is there another reason for this? + ###Only necessary when self.check_values is False (==external dataset tool?: can this be abstracted out as part of being a datasouce tool?) + ### but we still want (ALWAYS) to wrap input datasets + ### (this should be checked to prevent overhead of creating a new object?) # Additionally, datasets go in the param dict. We wrap them such that # if the bare variable name is used it returns the filename (for # backwards compatibility). We also add any child datasets to the diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Mon Feb 08 12:45:28 2010 -0500 @@ -31,11 +31,13 @@ """ input_datasets = dict() def visitor( prefix, input, value, parent = None ): - def process_dataset( data ): - if data and not isinstance( data.datatype, input.formats ): + def process_dataset( data, formats = None ): + if formats is None: + formats = input.formats + if data and not isinstance( data.datatype, formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) - target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) ) + target_ext, converted_dataset = data.find_conversion_destination( formats, converter_safe = input.converter_safe( param_values, trans ) ) if target_ext: if converted_dataset: data = converted_dataset @@ -61,16 +63,41 @@ # are stored as name1, name2, ... for i, v in enumerate( value ): input_datasets[ prefix + input.name + str( i + 1 ) ] = process_dataset( v ) + converters = [] + for converter_name, converter_extensions, converter_datatypes in input.converters: + new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], converter_datatypes ) + if not new_data or isinstance( new_data.datatype, converter_datatypes ): + input_datasets[ prefix + converter_name + str( i + 1 ) ] = new_data + converters.append( ( converter_name, new_data ) ) + else: + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, converter_extensions ) if parent: parent[input.name] = input_datasets[ prefix + input.name + str( i + 1 ) ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + parent[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired else: param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + param_values[ converter_name ][i] = converter_data.id #a more robust way to determine JSONable value is desired else: input_datasets[ prefix + input.name ] = process_dataset( value ) - if parent: - parent[input.name] = input_datasets[ prefix + input.name ] - else: - param_values[input.name] = input_datasets[ prefix + input.name ] + converters = [] + for converter_name, converter_extensions, converter_datatypes in input.converters: + new_data = process_dataset( input_datasets[ prefix + input.name ], converter_datatypes ) + if not new_data or isinstance( new_data.datatype, converter_datatypes ): + input_datasets[ prefix + converter_name ] = new_data + converters.append( ( converter_name, new_data ) ) + else: + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, converter_extensions ) + target_dict = parent + if not target_dict: + target_dict = param_values + target_dict[ input.name ] = input_datasets[ prefix + input.name ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + target_dict[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired tool.visit_inputs( param_values, visitor ) return input_datasets diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Mon Feb 08 12:45:28 2010 -0500 @@ -50,14 +50,14 @@ def get_html( self, trans=None, value=None, other_values={}): """ - Returns the html widget corresponding to the paramter. + Returns the html widget corresponding to the parameter. Optionally attempt to retain the current value specific by 'value' """ return self.get_html_field( trans, value, other_values ).get_html() def from_html( self, value, trans=None, other_values={} ): """ - Convert a value from an HTML POST into the parameters prefered value + Convert a value from an HTML POST into the parameters preferred value format. """ return value @@ -1168,6 +1168,15 @@ else: self.options = dynamic_options.DynamicOptions( options, self ) self.is_dynamic = self.options is not None + # Load converters required for the dataset input + self.converters = [] + for conv_elem in elem.findall( "converter" ): + name = conv_elem.get( "name" ) #name for commandline substitution + conv_extensions = conv_elem.get( "type" ) #target datatype extension + # FIXME: conv_extensions should be able to be an ordered list + assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) + conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ + self.converters.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): filter_value = None

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[hg] galaxy 3355: On edit attributes page, only sanitize and add...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/26f01eafc6bd changeset: 3355:26f01eafc6bd user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Feb 08 11:20:44 2010 -0500 description: On edit attributes page, only sanitize and add annotation when it exists. Metadata editing was throwing server error when not logged in. diffstat: lib/galaxy/web/controllers/root.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (15 lines): diff -r 4e8785b6815c -r 26f01eafc6bd lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Feb 08 10:00:30 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Mon Feb 08 11:20:44 2010 -0500 @@ -307,8 +307,9 @@ setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_setting_metadata( data ) # Sanitize annotation before adding it. - annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans, data, annotation ) + if params.annotation: + annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, data, annotation ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' trans.sa_session.flush()

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[hg] galaxy 3354: Fix from Assaf Gordon for Cheetah syntax error...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e8785b6815c changeset: 3354:4e8785b6815c user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Feb 08 10:00:30 2010 -0500 description: Fix from Assaf Gordon for Cheetah syntax errors in the Bar Chart tool. diffstat: tools/plotting/bar_chart.py | 1 - tools/plotting/bar_chart.xml | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diffs (25 lines): diff -r 390dfb039df7 -r 4e8785b6815c tools/plotting/bar_chart.py --- a/tools/plotting/bar_chart.py Mon Feb 08 09:53:20 2010 -0500 +++ b/tools/plotting/bar_chart.py Mon Feb 08 10:00:30 2010 -0500 @@ -23,7 +23,6 @@ """ -from Numeric import * import Gnuplot, Gnuplot.funcutils import sys, string, tempfile, os diff -r 390dfb039df7 -r 4e8785b6815c tools/plotting/bar_chart.xml --- a/tools/plotting/bar_chart.xml Mon Feb 08 09:53:20 2010 -0500 +++ b/tools/plotting/bar_chart.xml Mon Feb 08 10:00:30 2010 -0500 @@ -1,8 +1,8 @@ <tool id="barchart_gnuplot" name="Bar chart"> <description>for multiple columns</description> <command interpreter="python"> - #if $xtic.userSpecified == "Yes": #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" - #else: #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" + #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" + #else #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" #end if </command> <inputs>

1 0

[hg] galaxy 3353: Refactoring grid code: moved numerous grid col...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/390dfb039df7 changeset: 3353:390dfb039df7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 08 09:53:20 2010 -0500 description: Refactoring grid code: moved numerous grid column definitions from controller.py to grids.py diffstat: lib/galaxy/web/base/controller.py | 83 -------------------------- lib/galaxy/web/controllers/admin.py | 6 +- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 8 +- lib/galaxy/web/controllers/library_admin.py | 2 +- lib/galaxy/web/controllers/page.py | 28 ++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 4 +- lib/galaxy/web/controllers/workflow.py | 4 +- lib/galaxy/web/framework/helpers/grids.py | 89 ++++++++++++++++++++++++++- 10 files changed, 113 insertions(+), 115 deletions(-) diffs (465 lines): diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Feb 08 09:53:20 2010 -0500 @@ -9,41 +9,10 @@ from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.web.framework.helpers import grids -from galaxy.util.odict import odict from Cheetah.Template import Template log = logging.getLogger( __name__ ) - -# Useful columns in many grids used by controllers. - -class OwnerColumn( grids.TextColumn ): - """ Column that lists item's owner. """ - def get_value( self, trans, grid, item ): - return item.user.username - -class PublicURLColumn( grids.TextColumn ): - """ Column displays item's public URL based on username and slug. """ - def get_link( self, trans, grid, item ): - if item.user.username and item.slug: - return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - elif not item.user.username: - # TODO: provide link to set username. - return None - elif not item.user.slug: - # TODO: provide link to set slg - return None - -class DeletedColumn( grids.GridColumn ): - """ Column that tracks and filters for items with deleted attribute. """ - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class BaseController( object ): """ @@ -138,58 +107,6 @@ return True Root = BaseController - -class SharingStatusColumn( grids.GridColumn ): - """ Grid column to indicate sharing status. """ - def get_value( self, trans, grid, item ): - # Delete items cannot be shared. - if item.deleted: - return "" - - # Build a list of sharing for this item. - sharing_statuses = [] - if item.users_shared_with: - sharing_statuses.append( "Shared" ) - if item.importable: - sharing_statuses.append( "Accessible" ) - if item.published: - sharing_statuses.append( "Published" ) - return ", ".join( sharing_statuses ) - - def get_link( self, trans, grid, item ): - if not item.deleted and ( item.users_shared_with or item.importable or item.published ): - return dict( operation="share or publish", id=item.id ) - return None - - def filter( self, db_session, user, query, column_filter ): - """ Modify query to filter histories by sharing status. """ - if column_filter == "All": - pass - elif column_filter: - if column_filter == "private": - query = query.filter( self.model_class.users_shared_with == None ) - query = query.filter( self.model_class.importable == False ) - elif column_filter == "shared": - query = query.filter( self.model_class.users_shared_with != None ) - elif column_filter == "accessible": - query = query.filter( self.model_class.importable == True ) - elif column_filter == "published": - query = query.filter( self.model_class.published == True ) - return query - - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = odict() - accepted_filter_labels_and_vals["private"] = "private" - accepted_filter_labels_and_vals["shared"] = "shared" - accepted_filter_labels_and_vals["accessible"] = "accessible" - accepted_filter_labels_and_vals["published"] = "published" - accepted_filter_labels_and_vals["all"] = "All" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class Sharable: """ Mixin for a controller that manages and item that can be shared. """ diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -71,7 +71,7 @@ LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -159,7 +159,7 @@ UsersColumn( "Users", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -225,7 +225,7 @@ RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,7 +44,7 @@ model_class=model.FormDefinition, filterable="advanced" ), TypeColumn( "Type" ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,11 +44,11 @@ attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( @@ -118,7 +118,7 @@ return query.filter( model.HistoryUserShareAssociation.user == trans.user ) class HistoryAllPublishedGrid( grids.Grid ): - class NameURLColumn( PublicURLColumn, NameColumn ): + class NameURLColumn( grids.PublicURLColumn, NameColumn ): pass title = "Published Histories" @@ -128,7 +128,7 @@ use_async = True columns = [ NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -52,7 +52,7 @@ grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:53:20 2010 -0500 @@ -16,7 +16,7 @@ class PageListGrid( grids.Grid ): # Custom column. - class URLColumn( PublicURLColumn ): + class URLColumn( grids.PublicURLColumn ): def get_value( self, trans, grid, item ): return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) @@ -30,7 +30,7 @@ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -62,8 +62,8 @@ default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] @@ -100,8 +100,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -144,8 +144,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -167,8 +167,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -192,8 +192,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -212,8 +212,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:53:20 2010 -0500 @@ -95,7 +95,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), TypeColumn( "Type" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -107,7 +107,7 @@ TypeColumn( "Type", link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ), ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -184,7 +184,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.request_form.id ) ) ), ), SampleFormColumn( "Sample Form", link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.sample_form.id ) ) ), ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:53:20 2010 -0500 @@ -59,8 +59,8 @@ default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:53:20 2010 -0500 @@ -5,6 +5,7 @@ from galaxy.tags.tag_handler import TagHandler from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.odict import odict import sys, logging, math @@ -329,8 +330,8 @@ accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters -# Generic column that employs freetext and, hence, supports freetext, case-independent filtering. class TextColumn( GridColumn ): + """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ def filter( self, db_session, user, query, column_filter ): """ Modify query to filter using free text, case independence. """ if column_filter == "All": @@ -350,8 +351,8 @@ clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) return and_( *clause_list ) -# Column that supports community tags. class CommunityTagsColumn( TextColumn ): + """ Column that supports community tags. """ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class @@ -386,8 +387,8 @@ clause_list.append( self.model_class.tags.any( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ) ) ) return and_( *clause_list ) -# Column that supports individual tags. class IndividualTagsColumn( CommunityTagsColumn ): + """ Column that supports individual tags. """ def get_value( self, trans, grid, item ): return trans.fill_template( "/tagging_common.mako", tag_type="individual", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter" ) @@ -408,8 +409,8 @@ clause_list.append( self.model_class.tags.any( and_( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ), self.model_tag_association_class.user == user ) ) ) return and_( *clause_list ) -# Column that performs multicolumn filtering. class MulticolFilterColumn( TextColumn ): + """ Column that performs multicolumn filtering. """ def __init__( self, col_name, cols_to_filter, key, visible, filterable="default" ): GridColumn.__init__( self, col_name, key=key, visible=visible, filterable=filterable) self.cols_to_filter = cols_to_filter @@ -432,6 +433,86 @@ complete_filter = or_( *clause_list ) return query.filter( complete_filter ) + +class OwnerColumn( TextColumn ): + """ Column that lists item's owner. """ + def get_value( self, trans, grid, item ): + return item.user.username + +class PublicURLColumn( TextColumn ): + """ Column displays item's public URL based on username and slug. """ + def get_link( self, trans, grid, item ): + if item.user.username and item.slug: + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + elif not item.user.username: + # TODO: provide link to set username. + return None + elif not item.user.slug: + # TODO: provide link to set slg + return None + +class DeletedColumn( GridColumn ): + """ Column that tracks and filters for items with deleted attribute. """ + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters + +class SharingStatusColumn( GridColumn ): + """ Grid column to indicate sharing status. """ + def get_value( self, trans, grid, item ): + # Delete items cannot be shared. + if item.deleted: + return "" + + # Build a list of sharing for this item. + sharing_statuses = [] + if item.users_shared_with: + sharing_statuses.append( "Shared" ) + if item.importable: + sharing_statuses.append( "Accessible" ) + if item.published: + sharing_statuses.append( "Published" ) + return ", ".join( sharing_statuses ) + + def get_link( self, trans, grid, item ): + if not item.deleted and ( item.users_shared_with or item.importable or item.published ): + return dict( operation="share or publish", id=item.id ) + return None + + def filter( self, db_session, user, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( self.model_class.users_shared_with == None ) + query = query.filter( self.model_class.importable == False ) + elif column_filter == "shared": + query = query.filter( self.model_class.users_shared_with != None ) + elif column_filter == "accessible": + query = query.filter( self.model_class.importable == True ) + elif column_filter == "published": + query = query.filter( self.model_class.published == True ) + return query + + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["accessible"] = "accessible" + accepted_filter_labels_and_vals["published"] = "published" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False, confirm=None ):

1 0

[hg] galaxy 3352: Bug fixes to slug editing, tooltips, and click...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/aa81684b9275 changeset: 3352:aa81684b9275 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 08 09:03:07 2010 -0500 description: Bug fixes to slug editing, tooltips, and click-to-edit elements. diffstat: lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/page.py | 2 +- lib/galaxy/web/controllers/workflow.py | 2 +- static/june_2007_style/base.css.tmpl | 6 +++--- static/june_2007_style/blue/base.css | 4 ++-- static/scripts/autocomplete_tagging.js | 9 +++++++-- static/scripts/galaxy.base.js | 7 +++++++ static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/trackster.js | 2 +- templates/root/history.mako | 6 +++--- templates/sharing_base.mako | 2 +- templates/tagging_common.mako | 26 ++++++++++++-------------- 13 files changed, 41 insertions(+), 31 deletions(-) diffs (246 lines): diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500 @@ -405,7 +405,7 @@ if history: history.slug = new_slug trans.sa_session.flush() - return + return history.slug @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500 @@ -547,7 +547,7 @@ if page: page.slug = new_slug trans.sa_session.flush() - return + return page.slug @web.expose @web.json diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500 @@ -389,7 +389,7 @@ if stored: stored.slug = new_slug trans.sa_session.flush() - return + return stored.slug @web.expose @web.json diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Feb 05 23:03:03 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Feb 08 09:03:07 2010 -0500 @@ -718,7 +718,7 @@ cursor: pointer; } -.tooltip span.tip { +span.tip { display: none } @@ -726,8 +726,8 @@ font-size: 90%; display: block; position: absolute; - right:2em;top:-1.75em; - width: inherit; + left:2em; + bottom:1.75em; background-color: black; color: white; text-align: center; diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Feb 05 23:03:03 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Feb 08 09:03:07 2010 -0500 @@ -120,7 +120,7 @@ .icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} .icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} .tooltip {position: relative; cursor: pointer} -.tooltip span.tip{display: none;} -.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;right:2em;top:-1.75em; width: inherit; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} +span.tip{display: none;} +.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;left:3em;bottom:1.75em; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} .editable-text{cursor:pointer} .editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right} \ No newline at end of file diff -r 60308825b252 -r aa81684b9275 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500 @@ -259,6 +259,7 @@ add_tag_button.show(); tag_input_field.hide(); tag_area.removeClass("active-tag-area"); + tag_area.addClass("tooltip"); } else { @@ -273,11 +274,14 @@ // If a "delete image" object was pressed and area is inactive, do nothing. if ($(e.target).hasClass("delete-tag-img") && !is_active) - return false; + return false; // If a "tag name" object was pressed and area is inactive, do nothing. if ($(e.target).hasClass("tag-name") && !is_active) - return false; + return false; + + // Remove tooltip. + $(this).removeClass("tooltip"); // Hide add tag button, show tag_input field. Change background to show // area is active. @@ -299,6 +303,7 @@ { tag_area.blur(); $(document).unbind("click", handle_document_click); + $(this).addClass("tooltip"); } }; // TODO: we should attach the click handler to all frames in order to capture diff -r 60308825b252 -r aa81684b9275 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/galaxy.base.js Mon Feb 08 09:03:07 2010 -0500 @@ -229,9 +229,13 @@ t.blur( function() { $(this).remove(); $("#" + text_elt_id).show(); + if (has_tooltip) + tooltip_elt.addClass("tooltip"); if (on_finish != null) on_finish(t); }); + var has_tooltip = $(this).hasClass("tooltip"); + var tooltip_elt = $(this); t.keyup( function( e ) { if ( e.keyCode == 27 ) { // Escape key @@ -268,6 +272,9 @@ t.insertAfter( $("#" + text_elt_id) ); t.focus(); t.select(); + + // Remove tooltip so that it doesn't show during editing. + $(this).removeClass("tooltip"); return false; }); diff -r 60308825b252 -r aa81684b9275 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500 @@ -1,1 +1,1 @@ -function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" Tags":" Tag")}else{t="Add tags"}return t},tag_click_fn:function(r,s){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var e=jQuery.extend(g,q);var o=function(r){if(r.length){return r.length}var s=0;for(element in r){s++}return s};var h=$(this);var c=h.find(".tag-area");var f=h.find(".toggle-link");var b=h.find(".tag-input");var n=h.find(".add-tag-button");f.click(function(){var r=(c.css("display")=="none");var s;if(r){s=function(){var t=$(this).find(".tag-button").length;if(t==0){c.click()}}}else{s=func tion(){c.blur()}}c.slideToggle("fast",s);return $(this)});if(e.editable){b.hide()}b.keyup(function(w){if(w.keyCode==27){$(this).trigger("blur")}else{if((w.keyCode==13)||(w.keyCode==188)||(w.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((w.keyCode==188)||(w.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var t=k(new_value);var s=c.children(".tag-button");if(s.length!=0){var x=s.slice(s.length-1);x.after(t)}else{c.prepend(t)}var r=new_value.split(":");e.tags[r[0]]=r[1];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);var v=$(this);$.ajax({url:e.ajax_add_tag_url,data:{new_tag:new_value},error:function(){t.remove();delete e.tags[r[0]];var y=e.get_toggle_link_te xt_fn(e.tags);f.text(y);alert("Add tag failed")},success:function(){v.flushCache()}});return false}}});var j=function(t,s,r,v,u){tag_name_and_value=v.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var i={selectFirst:false,formatItem:j,autoFill:false,highlight:false};b.autocomplete(e.ajax_autocomplete_tag_url,i);h.find(".delete-tag-img").each(function(){d($(this))});init_tag_click_function($(this),e.tag_click_fn);n.click(function(){$(this).hide();c.click();return false});if(e.editable){c.blur(function(r){p=o(e.tags);if(p!=0){n.show();b.hide();c.removeClass("active-tag-area")}else{}});c.click(function(t){var s=$(this).hasClass("active-tag-area");if($(t.target).hasClass("delete-tag-img")&&!s){return false}if($(t.target).hasClass("tag-name")&&!s){return false}$(this).addClass("active-tag-area");n.hide();b.show();b.focus();var r=function(v){var u=c.attr("id");if(($(v.target).attr("id")!=u)&&($(v.target).parents().filter(u).length==0)) {c.blur();$(document).unbind("click",r)}};$(window).click(r);return false})}if(e.use_toggle_link){c.hide()}else{var p=o(e.tags);if(p==0){n.hide();b.show()}}function l(s,r){return s+((r!=""&&r)?":"+r:"")}function d(r){$(r).mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});$(r).mouseleave(function(){$(this).attr("src",e.delete_tag_img)});$(r).click(function(){var x=$(this).parent();var w=x.find(".tag-name").eq(0);var v=w.text();var t=m(v);var z=t[0];var s=t[1];var y=x.prev();x.remove();delete e.tags[z];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);$.ajax({url:e.ajax_delete_tag_url,data:{tag_name:z},error:function(){e.tags[z]=s;if(y.hasClass("tag-button")){y.after(x)}else{c.prepend(x)}var A=e.get_toggle_link_text_fn(e.tags);alert("Remove tag failed");f.text(A);r.mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});r.mouseleave(function(){$(this).attr("src",e.delete_tag_img)})},success:function(){}});return true})}function a(r){var s=new Array();for(key in r){s[s.length]=key+"-->"+r[key]}return"{"+s.join(",")+"}"}function m(r){return r.split(":")}function k(r){var s=$("<img src='"+e.delete_tag_img+"'/>").addClass("delete-tag-img");d(s);var t=$("<span>").text(r).addClass("tag-name");t.click(function(){tag_name_and_value=r.split(":");e.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var u=$("<span></span>").addClass("tag-button");u.append(t);if(e.editable){u.append(s)}return u}}; \ No newline at end of file +function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" Tags":" Tag")}else{t="Add tags"}return t},tag_click_fn:function(r,s){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var e=jQuery.extend(g,q);var o=function(r){if(r.length){return r.length}var s=0;for(element in r){s++}return s};var h=$(this);var c=h.find(".tag-area");var f=h.find(".toggle-link");var b=h.find(".tag-input");var n=h.find(".add-tag-button");f.click(function(){var r=(c.css("display")=="none");var s;if(r){s=function(){var t=$(this).find(".tag-button").length;if(t==0){c.click()}}}else{s=func tion(){c.blur()}}c.slideToggle("fast",s);return 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2010 -0500 +++ b/static/scripts/packed/trackster.js Mon Feb 08 09:03:07 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var 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d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.lo w<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this .content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.widt h(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.he ight_px+55+"px"});e.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(!this.vertical_range){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f }}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_val ue);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dat aset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end -d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined ){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.vie w.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P); p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=func tion(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.lengt h;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_i mg_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},add_label_track:function (a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){delete this.tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){f or(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.v iew.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div. addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{i nit:function(){this.data_queue={};this.data_cache=new Cache(CACHED_DATA);var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;if($("#linetrack_"+b +"_minval").length===0){var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)}a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top: 0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#trac k_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",l abel_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.adClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.get JSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(thi s.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slo ts[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e =$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0 ).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 60308825b252 -r aa81684b9275 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/root/history.mako Mon Feb 08 09:03:07 2010 -0500 @@ -43,7 +43,7 @@ })); // Rename management. - async_save_text("history-name", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); + async_save_text("history-name-container", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); // Tag management. $('#history-tag').click( function() @@ -57,7 +57,7 @@ $('#history-annotation-area').toggle("fast"); return false; }); - async_save_text("history-annotation", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); + async_save_text("history-annotation-container", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); // Updater updater({ @@ -322,7 +322,7 @@ ## Annotation elt. <div id="history-annotation-area" class="form-row" style="display: none"> <label>Annotation / Notes:</label> - <div class="tooltip"> + <div id="history-annotation-container" class="tooltip"> %if annotation: <span id="history-annotation">${annotation | h}</span> %else: diff -r 60308825b252 -r aa81684b9275 templates/sharing_base.mako --- a/templates/sharing_base.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/sharing_base.mako Mon Feb 08 09:03:07 2010 -0500 @@ -49,7 +49,7 @@ }; <% controller_name = get_controller_name( item ) %> - async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", false, 0, on_start, on_finish); + async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", null, false, 0, on_start, on_finish); }); </script> </%def> diff -r 60308825b252 -r aa81684b9275 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/tagging_common.mako Mon Feb 08 09:03:07 2010 -0500 @@ -37,7 +37,7 @@ %if use_toggle_link: <a class="toggle-link" href="#">${num_tags} Tag${iff( num_tags == 1, "", "s")}</a> %endif - <div class="tag-area + <div class="tag-area tooltip %if tag_type == 'individual': individual-tag-area %endif @@ -72,20 +72,18 @@ %endfor ## Add tag input field. If element is in form, tag input is a textarea; otherwise element is a input type=text. - <div class="tooltip"> - %if editable: - %if in_form: - <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> - %else: - <input class="tag-input" type='text' size='${input_size}'/> - %endif - ## Add "add tag" button. - %if render_add_tag_button: - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> - %endif + %if editable: + %if in_form: + <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> + %else: + <input class="tag-input" type='text' size='${input_size}'/> %endif - <span class="tip">Click to add tags</span> - </div> + ## Add "add tag" button. + %if render_add_tag_button: + <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %endif + <span class="tip">Click to edit tags</span> + %endif </div> </div> </%def>

1 0

[hg] galaxy 3351: python2.4 sha.new() cannot be based to hmac - ...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/60308825b252 changeset: 3351:60308825b252 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Fri Feb 05 23:03:03 2010 -0500 description: python2.4 sha.new() cannot be based to hmac - this patch tested with 2.4 and 2.5 diffstat: lib/galaxy/util/hash_util.py | 11 ++++++----- 1 files changed, 6 insertions(+), 5 deletions(-) diffs (30 lines): diff -r 4af74d038535 -r 60308825b252 lib/galaxy/util/hash_util.py --- a/lib/galaxy/util/hash_util.py Fri Feb 05 19:35:52 2010 -0500 +++ b/lib/galaxy/util/hash_util.py Fri Feb 05 23:03:03 2010 -0500 @@ -6,15 +6,16 @@ import sys, logging # Use hashlib module if for Python 2.5+, fall back on old sha and md5 modules +# sha1 requires explicit calls to new if also being passed to hmac (!) try: import hashlib sha1 = hashlib.sha1 + sha = sha1 md5 = hashlib.md5 except ImportError, e: - import sha, md5 - sha1 = sha.new - md5 = md5.new - + from sha import new as sha1 + import sha + from md5 import new as md5 import hmac log = logging.getLogger( __name__ ) @@ -30,4 +31,4 @@ return sha1() def hmac_new( key, value ): - return hmac.new( key, value, sha1 ).hexdigest() + return hmac.new( key, value, sha ).hexdigest()

1 0

[hg] galaxy 3350: typo
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4af74d038535 changeset: 3350:4af74d038535 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 05 19:35:52 2010 -0500 description: typo diffstat: lib/galaxy/web/controllers/tracks.py | 6 +++++- 1 files changed, 5 insertions(+), 1 deletions(-) diffs (16 lines): diff -r 432a32ba55bb -r 4af74d038535 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:35:52 2010 -0500 @@ -121,7 +121,11 @@ latest_revision = vis.latest_revision tracks = [] - dbkey = latest_revision.config['dbkey'] + try: + dbkey = latest_revision.config['dbkey'] + except KeyError: + dbkey = None + hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id']

1 0

[hg] galaxy 3349: trackster:
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/432a32ba55bb changeset: 3349:432a32ba55bb user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 05 19:08:37 2010 -0500 description: trackster: - New interface for new track browsers - Saving shows progress bar - Can now add tracks async - Switching dbkeys is now async diffstat: lib/galaxy/web/controllers/tracks.py | 128 ++++------ lib/galaxy/web/controllers/visualization.py | 2 +- static/scripts/trackster.js | 61 +++- static/trackster.css | 1 + templates/grid_base.mako | 4 + templates/tracks/add_tracks.mako | 3 +- templates/tracks/browser.mako | 344 ++++++++++++++++----------- templates/tracks/index.mako | 52 +++- templates/tracks/new_browser.mako | 81 +----- 9 files changed, 359 insertions(+), 317 deletions(-) diffs (955 lines): diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 16:34:30 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500 @@ -57,10 +57,7 @@ use_paging = False columns = [ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), - # grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Filetype", key="extension" ), - # Columns that are valid for filtering but are not visible. - # SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" ) ] def apply_default_filter( self, trans, query, **kwargs ): if self.available_tracks is None: @@ -80,62 +77,40 @@ @web.expose def index( self, trans ): - return trans.fill_template( "tracks/index.mako" ) - + config = {} + + return trans.fill_template( "tracks/browser.mako", config=config ) + @web.expose @web.require_login() - def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ): - """ - Build a new browser from datasets in the current history. Redirects - to 'browser' once datasets to browse have been selected. - """ - session = trans.sa_session - # If the user clicked the submit button explicitly, try to build the browser - if title and browse and dataset_ids: - if not isinstance( dataset_ids, list ): - dataset_ids = [ dataset_ids ] - # Build config - tracks = [] - for dataset_id in dataset_ids: - tracks.append( { "dataset_id": str( dataset_id ) } ) - config = { "tracks": tracks } - # Build visualization object - vis = model.Visualization() - vis.user = trans.user - vis.title = title - vis.type = "trackster" - vis_rev = model.VisualizationRevision() - vis_rev.visualization = vis - vis_rev.title = title - vis_rev.config = config - vis.latest_revision = vis_rev - session.add( vis ) - session.add( vis_rev ) - session.flush() - trans.response.send_redirect( web.url_for( controller='tracks', action='browser', id=trans.security.encode_id( vis.id ) ) ) + def new_browser( self, trans ): + dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] + dbkey_set = set( dbkeys ) + if not dbkey_set: + return trans.show_error_message( "Current history has no valid datasets to visualize." ) else: - # Determine the set of all dbkeys that are used in the current history - dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] - dbkey_set = set( dbkeys ) - if not dbkey_set: - return trans.show_error_message( "Current history has no valid datasets to visualize." ) - - # If a dbkey argument was not provided, or is no longer valid, default - # to the first one - if dbkey is None or dbkey not in dbkey_set: - dbkey = dbkeys[0] - # Find all datasets in the current history that are of that dbkey - # and can be displayed - datasets = {} - if self.available_tracks is None: - self.available_tracks = trans.app.datatypes_registry.get_available_tracks() - for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and dataset.extension in self.available_tracks: - datasets[dataset.id] = (dataset.extension, dataset.name) - # Render the template - return trans.fill_template( "tracks/new_browser.mako", available_tracks=self.available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) - + return trans.fill_template( "tracks/new_browser.mako", dbkey_set=dbkey_set ) + + @web.json + @web.require_login() + def add_track_async(self, trans, id): + dataset_id = trans.security.decode_id( id ) + + hda_query = trans.sa_session.query( model.HistoryDatasetAssociation ) + dataset = hda_query.get( dataset_id ) + track_type, indexer = dataset.datatype.get_track_type() + + track = { + "track_type": track_type, + "indexer": indexer, + "name": dataset.name, + "dataset_id": dataset.id, + "prefs": {}, + } + return track + @web.expose + @web.require_login() def browser(self, trans, id, chrom=""): """ Display browser for the datasets listed in `dataset_ids`. @@ -143,8 +118,10 @@ decoded_id = trans.security.decode_id( id ) session = trans.sa_session vis = session.query( model.Visualization ).get( decoded_id ) + latest_revision = vis.latest_revision tracks = [] - dbkey = "" + + dbkey = latest_revision.config['dbkey'] hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] @@ -161,18 +138,10 @@ "dataset_id": dataset.id, "prefs": simplejson.dumps(prefs), } ) - dbkey = dataset.dbkey - chrom_lengths = self._chroms( trans, dbkey ) - if chrom_lengths is None: - error( "No chromosome lengths file found for '%s'" % dataset.name ) - return trans.fill_template( 'tracks/browser.mako', - #dataset_ids=dataset_ids, - title = vis.title, - id=id, - tracks=tracks, - chrom=chrom, - dbkey=dbkey, - LEN=chrom_lengths.get(chrom, 0) ) + if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat + + config = { "title": vis.title, "vis_id": id, "tracks": tracks, "chrom": chrom, "dbkey": dbkey } + return trans.fill_template( 'tracks/browser.mako', config=config ) @web.json def chroms(self, trans, dbkey=None ): @@ -288,9 +257,19 @@ @web.json def save( self, trans, **kwargs ): - decoded_id = trans.security.decode_id( kwargs['id'] ) session = trans.sa_session - vis = session.query( model.Visualization ).get( decoded_id ) + vis_id = kwargs['vis_id'].strip('"') + dbkey = kwargs['dbkey'] + + if vis_id == "undefined": # new vis + vis = model.Visualization() + vis.user = trans.user + vis.title = kwargs['vis_title'] + vis.type = "trackster" + session.add( vis ) + else: + decoded_id = trans.security.decode_id( vis_id ) + vis = session.query( model.Visualization ).get( decoded_id ) decoded_payload = simplejson.loads( kwargs['payload'] ) vis_rev = model.VisualizationRevision() @@ -304,10 +283,11 @@ "track_type": track['track_type'], "prefs": track['prefs'] } ) - vis_rev.config = { "tracks": tracks } + vis_rev.config = { "dbkey": dbkey, "tracks": tracks } vis.latest_revision = vis_rev session.add( vis_rev ) session.flush() + return trans.security.encode_id(vis.id) data_grid = DatasetSelectionGrid() @@ -316,11 +296,5 @@ def list_datasets( self, trans, **kwargs ): """List all datasets that can be added as tracks""" - # Render the list view - # return trans.fill_template( 'tracks/add_tracks.mako', grid=data_grid( trans, status=status, message=message, **kwargs ) ) return self.data_grid( trans, **kwargs ) - - # - - \ No newline at end of file diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Fri Feb 05 16:34:30 2010 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Fri Feb 05 19:08:37 2010 -0500 @@ -7,7 +7,7 @@ # Grid definition title = "Visualizations" model_class = model.Visualization - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ grids.GridColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), diff -r 99483ae6c738 -r 432a32ba55bb static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Feb 05 16:34:30 2010 -0500 +++ b/static/scripts/trackster.js Fri Feb 05 19:08:37 2010 -0500 @@ -77,14 +77,16 @@ } }); -var View = function( chrom, max_high, config ) { +var View = function( chrom, title, vis_id, dbkey ) { + this.vis_id = vis_id; + this.dbkey = dbkey; + this.title = title; this.chrom = chrom; - this.config = config; this.tracks = []; + this.label_tracks = []; this.max_low = 0; - this.max_high = max_high; + this.max_high = 0; this.center = (this.max_high - this.max_low) / 2; - this.span = this.max_high - this.max_low; this.zoom_factor = 3; this.zoom_level = 0; }; @@ -94,6 +96,10 @@ this.tracks.push( track ); if (track.init) { track.init(); } }, + add_label_track: function ( label_track ) { + label_track.view = this; + this.label_tracks.push( label_track ); + }, remove_track: function( track ) { delete this.tracks[track]; }, @@ -105,7 +111,8 @@ } } }, - redraw: function() { + redraw: function(nodraw) { + this.span = this.max_high - this.max_low; var span = this.span / Math.pow(this.zoom_factor, this.zoom_level), low = this.center - (span / 2), high = low + span; @@ -134,11 +141,14 @@ }).show(); $("#low").val( commatize(this.low) ); $("#high").val( commatize(this.high) ); - for ( var i = 0, len = this.tracks.length; i < len; i++ ) { - this.tracks[i].draw(); + if (!nodraw) { + for ( var i = 0, len = this.tracks.length; i < len; i++ ) { + this.tracks[i].draw(); + } + for ( var i = 0, len = this.label_tracks.length; i < len; i++ ) { + this.label_tracks[i].draw(); + } } - //$("#bottom-spacer").remove(); - //$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>'); }, zoom_in: function ( point ) { if (this.max_high === 0 || this.high - this.low < 30) { @@ -238,6 +248,7 @@ var LabelTrack = function ( parent_element ) { Track.call( this, null, parent_element ); + this.track_type = "LabelTrack"; this.hidden = true; this.container_div.addClass( "label-track" ); }; @@ -273,26 +284,27 @@ this.height_px = 100; this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; - this.data_queue = {}; - this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of - // asynchronous calls this.prefs = { 'min_value': undefined, 'max_value': undefined }; if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { + this.data_queue = {}; + this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of + // asynchronous calls var track = this, track_id = track.view.tracks.indexOf(track); - + track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); $.getJSON( data_url, { stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { track.container_div.addClass("error"); track.content_div.text(DATA_ERROR); - } else if (data == "no data") { + } else if (data.length === 0 || data == "no data") { track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (data == "pending") { @@ -313,15 +325,17 @@ } track.vertical_range = track.prefs.max_value - track.prefs.min_value; - // Draw y-axis labels - var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); - var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); + // Draw y-axis labels if necessary + if ( $('#linetrack_' + track_id + '_minval').length === 0) { + var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); - max_label.css({ position: "relative", top: "25px" }); - max_label.prependTo(track.container_div); + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); - min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); - min_label.prependTo(track.container_div); + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); + min_label.prependTo(track.container_div); + } track.draw(); } @@ -345,7 +359,7 @@ } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - if (!this.vertical_range) { // We don't have the necessary information yet + if (this.vertical_range === undefined) { // We don't have the necessary information yet return; } @@ -463,6 +477,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { @@ -473,7 +488,7 @@ track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (data == "pending") { - track.container_div.addClass("pending"); + track.container_div.adClass("pending"); track.content_div.text(DATA_PENDING); setTimeout(function() { track.init(); }, 5000); } else { diff -r 99483ae6c738 -r 432a32ba55bb static/trackster.css --- a/static/trackster.css Fri Feb 05 16:34:30 2010 -0500 +++ b/static/trackster.css Fri Feb 05 19:08:37 2010 -0500 @@ -8,6 +8,7 @@ #nav-container { position: fixed; + left: 0; bottom: 0; } diff -r 99483ae6c738 -r 432a32ba55bb templates/grid_base.mako --- a/templates/grid_base.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/grid_base.mako Fri Feb 05 19:08:37 2010 -0500 @@ -27,6 +27,10 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${self.grid_javascripts()} +</%def> + +<%def name="grid_javascripts()"> ${h.js("jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> ## TODO: generalize and move into galaxy.base.js diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/add_tracks.mako --- a/templates/tracks/add_tracks.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/add_tracks.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,8 +1,9 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> -${javascripts()} ${stylesheets()} +${grid_javascripts()} + ${render_grid_table( grid, show_item_checkboxes=True )} ## Initialize the grid. diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/browser.mako Fri Feb 05 19:08:37 2010 -0500 @@ -45,7 +45,7 @@ </div> </div> -<div id="nav-container"> +<div id="nav-container" style="width:100%;"> <div id="nav-labeltrack"></div> <div id="nav"> <div id="overview"> @@ -59,8 +59,7 @@ <option value="">Loading</option> </select> <input id="low" size="12" />:<input id="high" size="12" /> - ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> - <input type="hidden" name="id" value="${id}" /> + <input type="hidden" name="id" value="${config.get('vis_id', '')}" /> <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> @@ -75,11 +74,10 @@ <div class="unified-panel-header-inner">Configuration</div> </div> <form action="${h.url_for( action='update_config' )}"> -## <input name="title" id="title" value="${title}" /> +## <input name="title" id="title" value="${config.title}" /> <div id="show-hide-move"> <ul id="sortable-ul"></ul> </div> -## <input type="submit" id="update-config" value="Save settings" /> <input type="button" id="refresh-button" value="Refresh" /> <input type="button" id="save-button" value="Save" /> <input id="add-track" type="button" value="Add Track" /> @@ -89,154 +87,227 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} +${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} <script type="text/javascript"> var data_url = "${h.url_for( action='data' )}"; - var view = new View( "${chrom}", ${LEN} ); + var view; $(function() { - view.add_track( new LabelTrack( $("#top-labeltrack" ) ) ); - view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); - - %for track in tracks: - view.add_track( - new ${track["track_type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} ) - ); - %endfor - - $(document).bind( "redraw", function( e ) { - view.redraw(); - }); - - $("#content").bind("mousewheel", function( e, delta ) { - if (delta > 0) { - view.zoom_in(e.pageX); - } else { - view.zoom_out(); - } - e.preventDefault(); - }); - - $("#content").bind("dblclick", function( e ) { - view.zoom_in(e.pageX); - }); - - // To let the overview box be draggable - $("#overview-box").bind("dragstart", function( e ) { - this.current_x = e.offsetX; - }).bind("drag", function( e ) { - var delta = e.offsetX - this.current_x; - this.current_x = e.offsetX; - - var delta_chrom = Math.round(delta / $(document).width() * view.span); - view.center += delta_chrom; - view.redraw(); - }); - - // To adjust the size of the viewport to fit the fixed-height footer - var refresh = function( e ) { - $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); - $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); - $("#nav-container").width( $("#center").width() ); - view.redraw(); - }; - $(window).bind( "resize", function(e) { refresh(e); } ); - $("#right-border").bind( "click", function(e) { refresh(e); } ); - $("#right-border").bind( "dragend", function(e) { refresh(e); } ); - $(window).trigger( "resize" ); - - $("#viewport").bind( "dragstart", function( e ) { - this.original_low = view.low; - this.current_height = e.clientY; - this.current_x = e.offsetX; - }).bind( "drag", function( e ) { - var container = $(this).parent(); - var delta = e.offsetX - this.current_x; - var new_scroll = container.scrollTop() - (e.clientY - this.current_height); - if ( new_scroll < container.get(0).scrollHeight - container.height() ) { - container.scrollTop(new_scroll); - } - this.current_height = e.clientY; - this.current_x = e.offsetX; - - var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); - view.center -= delta_chrom; - view.redraw(); - }); - - $("#refresh-button").bind( "click", function(e) { - view.update_options(); - }); - - // Use a popup grid to add more tracks - $("#add-track").bind( "click", function(e) { + %if config: + view = new View( "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + %for track in config.get('tracks'): + view.add_track( + new ${track["track_type"]}( "${track['name'] | h}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} ) + ); + %endfor + init(); + %else: $.ajax({ - url: "${h.url_for( action='list_datasets' )}", + url: "${h.url_for( action='new_browser' )}", data: {}, - error: function() { alert( "Grid refresh failed" ) }, - success: function(table_html) { - show_modal("Add Track — Select Dataset(s)", table_html, { - "Insert": function() { - hide_modal(); - }, - "Cancel": function() { + error: function() { alert( "Couldn't create new browser" ) }, + success: function(form_html) { + show_modal("New Track Browser", form_html, { + "Continue": function() { + view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() ); + init(); hide_modal(); } }); } }); - }); + %endif - $("#save-button").bind("click", function(e) { - view.update_options(); - var sorted = $("ul#sortable-ul").sortable('toArray'); - var payload = []; - for (var i in sorted) { - var track_id = parseInt(sorted[i].split("track_")[1]), - track = view.tracks[track_id]; - - payload.push( { - "track_type": track.track_type, - "indexer": track.indexer, - "name": track.name, - "dataset_id": track.dataset_id, - "prefs": track.prefs - }); - } - $.ajax({ - url: "${h.url_for( action='save' )}", - data: { - 'id': '${id}', - 'payload': JSON.stringify(payload) + // Execute this when everything is ready + function init() { + $("ul#sortable-ul").sortable({ + update: function(event, ui) { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + } } }); - }); - - // Execute this on page load - (function () { - $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: "${dbkey}" }, function ( data ) { + + $(document).bind( "redraw", function( e ) { + view.redraw(); + }); + + $("#content").bind("mousewheel", function( e, delta ) { + if (delta > 0) { + view.zoom_in(e.pageX); + } else { + view.zoom_out(); + } + e.preventDefault(); + }); + + $("#content").bind("dblclick", function( e ) { + view.zoom_in(e.pageX); + }); + + // To let the overview box be draggable + $("#overview-box").bind("dragstart", function( e ) { + this.current_x = e.offsetX; + }).bind("drag", function( e ) { + var delta = e.offsetX - this.current_x; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * view.span); + view.center += delta_chrom; + view.redraw(); + }); + + // To adjust the size of the viewport to fit the fixed-height footer + var refresh = function( e ) { + $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); + $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); + $("#nav-container").width( $("#center").width() ); + view.redraw(); + }; + $(window).bind( "resize", function(e) { refresh(e); } ); + $("#right-border").bind( "click", function(e) { refresh(e); } ); + $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $(window).trigger( "resize" ); + + $("#viewport").bind( "dragstart", function( e ) { + this.original_low = view.low; + this.current_height = e.clientY; + this.current_x = e.offsetX; + }).bind( "drag", function( e ) { + var container = $(this).parent(); + var delta = e.offsetX - this.current_x; + var new_scroll = container.scrollTop() - (e.clientY - this.current_height); + if ( new_scroll < container.get(0).scrollHeight - container.height() ) { + container.scrollTop(new_scroll); + } + this.current_height = e.clientY; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); + view.center -= delta_chrom; + view.redraw(); + }); + + $("#refresh-button").bind( "click", function(e) { + view.update_options(); + }); + + // Use a popup grid to add more tracks + $("#add-track").bind( "click", function(e) { + $.ajax({ + url: "${h.url_for( action='list_datasets' )}", + data: {}, + error: function() { alert( "Grid refresh failed" ) }, + success: function(table_html) { + show_modal("Add Track — Select Dataset(s)", table_html, { + "Insert": function() { + $('input[name=id]:checked').each(function() { + var item_id = $(this).val(); + $.ajax( { + url: "${h.url_for( action='add_track_async' )}", + data: { id: item_id }, + dataType: "json", + error: function() {}, + success: function(track_data) { + var new_track; + var td = track_data; + switch(track_data.track_type) { + case "LineTrack": + new_track = new LineTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + case "FeatureTrack": + new_track = new FeatureTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + case "ReadTrack": + new_track = new ReadTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + } + view.add_track(new_track); + sidebar_box(new_track); + } + }); + + }); + + hide_modal(); + }, + "Cancel": function() { + hide_modal(); + } + }); + } + }); + }); + + $("#save-button").bind("click", function(e) { + view.update_options(); + var sorted = $("ul#sortable-ul").sortable('toArray'); + var payload = []; + for (var i in sorted) { + var track_id = parseInt(sorted[i].split("track_")[1]), + track = view.tracks[track_id]; + + payload.push( { + "track_type": track.track_type, + "indexer": track.indexer, + "name": track.name, + "dataset_id": track.dataset_id, + "prefs": track.prefs + }); + } + // Show saving dialog box + show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); + + $.ajax({ + url: "${h.url_for( action='save' )}", + data: { + 'vis_id': view.vis_id, + 'vis_title': view.title, + 'dbkey': view.dbkey, + 'payload': JSON.stringify(payload) + }, + success: function(vis_id) { + view.vis_id = vis_id; + hide_modal(); + } + }); + }); + + view.add_label_track( new LabelTrack( $("#top-labeltrack" ) ) ); + view.add_label_track( new LabelTrack( $("#nav-labeltrack" ) ) ); + + $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: view.dbkey }, function ( data ) { + view.chrom_data = data; var chrom_options = '<option value="">Select Chrom/Contig</option>'; for (i in data) { - chrom = data[i]['chrom'] - if( chrom == view.chrom ) { - chrom_options += '<option value="' + chrom + '" selected="true">' + chrom + '</option>'; - } else { - chrom_options += '<option value="' + chrom + '">' + chrom + '</option>'; - } + var chrom = data[i]['chrom'] + chrom_options += '<option value="' + chrom + '">' + chrom + '</option>'; } $("#chrom").html(chrom_options); $("#chrom").bind( "change", function () { - $("#chr").submit(); + view.chrom = $("#chrom").val(); + var found = $.grep(view.chrom_data, function(v, i) { + return v.chrom === view.chrom; + })[0]; + view.max_high = found.len; + view.redraw(true); + + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (track.init) { + track.init(); + } + } + // view.redraw(); }); }); - // Populate sort/move ul - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; + function sidebar_box(track) { if (!track.hidden) { + var track_id = view.tracks.length -1; // Track was just added to view, so index is current length -1 var label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'); var title = $('<div class="historyItemTitle"></div>'); var del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'); @@ -255,18 +326,17 @@ li.append(div); $("ul#sortable-ul").append(li); } + }; + + // Populate sort/move ul + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + sidebar_box(track); } - $("ul#sortable-ul").sortable({ - update: function(event, ui) { - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; - } - } - }); - - })(); - $(window).trigger("resize"); + $(window).trigger("resize"); + }; + }); </script> diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/index.mako --- a/templates/tracks/index.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/index.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,16 +1,38 @@ -<%inherit file="/base_panels.mako"/> +<form id="form" method="POST"> + <div class="form-row"> + <label for="dbkey">Browser name:</label> + <div class="form-row-input"> + <input type="text" name="title" id="title" value="Unnamed Browser"></input> + </div> + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <label for="dbkey">Reference genome build (dbkey): </label> + <div class="form-row-input"> + <select name="dbkey" id="dbkey" refresh_on_change="true"> + %for tmp_dbkey in dbkey_set: + <option value="${tmp_dbkey}" + %if tmp_dbkey == dbkey: + selected="selected" + %endif + >${tmp_dbkey}</option> + %endfor + </select> + </div> + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> + %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): + <div> + <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> + <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> + </div> + %endfor -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="visualization" - self.message_box_visible=False -%> -</%def> - -<%def name="center_panel()"> - - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="tracks", action="new_browser" )}"> </iframe> - -</%def> \ No newline at end of file + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <input type="submit" name="browse" value="Browse"/> + </div> +</form> diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/new_browser.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,65 +1,20 @@ -<%inherit file="/base.mako"/> - -<%def name="javascripts()"> -${parent.javascripts()} -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - $("#form").submit(); - }); -}); -</script> -</%def> - -% if not available_tracks: - <div class="errormessagelarge"> - There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains - converters for datatypes (see tool_conf.xml.sample) for examples. +<form id="form" method="POST"> + <div class="form-row"> + <label for="title">Browser name:</label> + <div class="form-row-input"> + <input type="text" name="title" id="new-title" value="Unnamed Browser"></input> + </div> + <div style="clear: both;"></div> </div> - -% else: - <div class="form"> - <div class="form-title">Create new track browser</div> - - <div id="dbkey" class="form-body"> - <form id="form" method="POST"> - <div class="form-row"> - <label for="dbkey">Browser name:</label> - <div class="form-row-input"> - <input type="text" name="title" id="title" value="Unnamed Browser"></input> - </div> - <div style="clear: both;"></div> - </div> - <div class="form-row"> - <label for="dbkey">Reference genome build (dbkey): </label> - <div class="form-row-input"> - <select name="dbkey" id="dbkey" refresh_on_change="true"> - %for tmp_dbkey in dbkey_set: - <option value="${tmp_dbkey}" - %if tmp_dbkey == dbkey: - selected="selected" - %endif - >${tmp_dbkey}</option> - %endfor - </select> - </div> - <div style="clear: both;"></div> - </div> - <div class="form-row"> - <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> - %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): - <div> - <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> - <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> - </div> - %endfor - - <div style="clear: both;"></div> - </div> - </div> - <div class="form-row"> - <input type="submit" name="browse" value="Browse"/> - </div> - </form> + <div class="form-row"> + <label for="dbkey">Reference genome build (dbkey): </label> + <div class="form-row-input"> + <select name="dbkey" id="new-dbkey"> + %for dbkey in dbkey_set: + <option value="${dbkey}">${dbkey}</option> + %endfor + </select> + </div> + <div style="clear: both;"></div> </div> -% endif +</form>

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[hg] galaxy 3348: Prevent history tag and annotation icons from ...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/99483ae6c738 changeset: 3348:99483ae6c738 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 16:34:30 2010 -0500 description: Prevent history tag and annotation icons from wrapping. diffstat: templates/root/history.mako | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r 656e1014f2fa -r 99483ae6c738 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 16:27:18 2010 -0500 +++ b/templates/root/history.mako Fri Feb 05 16:34:30 2010 -0500 @@ -286,8 +286,8 @@ <span class="tip">Click to edit</span></a> </div> </td> - <td align="right"> - <div style="float: right"> + <td align="right" style="width: 40px"> + <div style="float: right; white-space: nowrap"> <a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> <a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> </div>

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[hg] galaxy 3347: Add a label for experiment name in MACs
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/656e1014f2fa changeset: 3347:656e1014f2fa user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 16:27:18 2010 -0500 description: Add a label for experiment name in MACs diffstat: tools/peak_calling/macs_wrapper.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r e9de35947c06 -r 656e1014f2fa tools/peak_calling/macs_wrapper.xml --- a/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:06:27 2010 -0500 +++ b/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:27:18 2010 -0500 @@ -6,7 +6,7 @@ <requirement type="binary">macs</requirement> </requirements> <inputs> - <param name="experiment_name" type="text" value="MACS in Galaxy" size="50"/> + <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/> <conditional name="input_type"> <param name="input_type_selector" type="select" label="Paired End Sequencing"> <option value="paired_end">Paired End (requires elandmultipet format)</option>

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